Override Bed Plot Colors

[Alex-Willenbrink]

Hello,

Currently, if you load a BED file in to the genome browser, you can only change the color of the plots if you did not specify color of your plots in the BED file. Can this behavior be changed, so we can override an initial specified plot color?

Thanks,

-Alex

[jrobinso]

@Alex-Willenbrink For clarification -- are you saying the menu item (set color) doesn't work if you set an initial color?

[Alex-Willenbrink]

@jrobinso Yes, the menu is one of the places that the color can't be changed BUT you also can't change the color of your plots even if you specify the color in the track object you pass into the "loadTrack" function.

For example if this is my bed file:
2 21016630 21016650 301012 1000 - 21016630 21016650 0,0,255 1 20, 0,

This plot will always show up as blue even if I add the "color" property in the track object.

[jrobinso]

OK, I would call that a bug, certainly not intended. Will fix.

…

On Thu, Feb 27, 2020 at 4:34 PM Alex Willenbrink ***@***.***> wrote: @jrobinso <https://github.com/jrobinso> Yes, the menu is one of the places that the color can't be changed BUT you also can't change the color of your plots even if you specify the color in the track object you pass into the "loadTrack" function. For example if this is my bed file: 2 21016630 21016650 301012 1000 - 21016630 21016650 0,0,255 1 20, 0, This plot will always show up as blue even if I add the "color" property in the track object. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1068?email_source=notifications&email_token=AAHD2HE64DXNINK5DKYJCETRFBLXPA5CNFSM4K4PHNSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENGQGWY#issuecomment-592249691>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HFDWE2WUFRWDFYFDPDRFBLXPANCNFSM4K4PHNSA> .

[Alex-Willenbrink]

Thanks! Also one last thing I promise, is there an eventHandler for track color changes? If not, how would you recommend we listen for the track color state changes?

[jrobinso]

No, and that's rather specific to add a handler for. Why do you want to catch this? I ask because there might be another way to accomplish what you are trying to do.

…

On Thu, Feb 27, 2020 at 4:49 PM Alex Willenbrink ***@***.***> wrote: Thanks! Also one last thing I promise, is there an eventHandler for track color changes? If not, how would you recommend we listen for the track color state change? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1068?email_source=notifications&email_token=AAHD2HEITVZKMHW5W5AUBETRFBNSRA5CNFSM4K4PHNSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENGRGFI#issuecomment-592253717>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HDX4Y6K7OTFIU64Z7LRFBNSRANCNFSM4K4PHNSA> .

[Alex-Willenbrink]

I'm trying to capture the state of the genome browser (genome, locus, tracks, track order, plot colors, etc.) in the URL so that users will be able to reproduce the same state of the genome browser if they wanted to copy the URL and revisit the link later or share it with another person.

[jrobinso]

Hi, we already have a method that does that, I just looked and realized its not documented. We use it to support links at igv.org/app, like this one: http://tinyurl.com/vrhmrtl

To use this first enable query parameters in your igv config

queryParametersSupported: true

You will construct a url for bookmarking / sharing something like this

urlToYourSite?sessionURL=blob:<igv blob string>

To get <igv blob string> call

browser.compressedSession()

Let me know how it works, AFAIK you might be the first besides ourselves to try it.

There is also a method to get a json representation of the session, but its not useful as a URL parameter.

[jrobinso]

I've updated the doc for this: https://github.com/igvteam/igv.js/wiki/Query-Parameters

[jrobinso]

Original issue duplicate of #994